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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (2): 506-513.doi: 10.3724/SP.J.1006.2024.31040

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Discovery of auxin pathway genes involving spike type and association analysis between TaARF23-A and spikelet number in wheat

TAN Dan(), CHEN Jia-Ting, GAO Yu, ZHANG Xiao-Jun, LI Xin, YAN Gui-Yun, LI Rui, CHEN Fang, CHANG Li-Fang, ZHANG Shu-Wei, GUO Hui-Juan, CHANG Zhi-Jian, QIAO Lin-Yi*()   

  1. College of Agriculture, Shanxi Agricultural University / Shanxi Key Laboratory of Crop Genetics and Molecular Improvement / Key Laboratory of Sustainable Dryland Agriculture (co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Taiyuan 030031, Shanxi, China
  • Received:2023-06-22 Accepted:2023-09-13 Online:2024-02-12 Published:2023-09-27
  • Contact: *E-mail: linyi.qiao@sxau.edu.cn
  • Supported by:
    National Natural Science Foundation of China(32201749);Shanxi Key Research and Development Program(202102140601001)

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Abstract:

Auxin is one of the major endogenous hormones that regulate the spike morphology in crops. In order to explore the auxin pathway genes involving spike type in wheat, the line SY95-71 with spindle spike and line CH7034 with compacted spike were selected to detect the endogenous auxin content in their young spikes. The results showed that the tryptophan content in SY95-71’s young spikes was significantly higher than that in CH7034. RNA-seq results showed that four specific auxin-related GO items were enriched in SY95-71 young spikes within the high confidence interval (P<0.01), and the relative expression levels of Tryptophan Decarboxylase genes (responsible for transforming tryptophan into tryptamine) and Auxin Response Factor genes (ARFs) in SY95-71 were significantly higher than those in CH7034. Further analysis of two highly expressed ARF genes (TraesCS7A02G475600 and TraesCS7A02G475700) in SY95-71 revealed that they were a pair of tandem repeat genes located on the long arm of chromosome 7A and named TaARF23-A1 and TaARF23-A2 based on the IDs of ARF family member in wheat, respectively. The qRT-PCR results confirmed that the relative expression levels of TaARF23-A1 and TaARF23-A2 in SY95-71 young spikes were significantly higher than those in CH7034. The sequencing results showed that the exon of TaARF23-A had two SNPs and one InDel site between SY95-71 and CH7034. A molecular marker was developed based on the InDel site and then used to associated with the spike phenotypes of the recombinant inbred lines population derived by the cross of SY95-71 and CH7034 in six field environments. The results showed that TaARF23-A was significant correlation with spikelet number (P<0.0001), and its CH7034 allele increased by 1.67 spikelets compared with the SY95-71 allele. The results of this study provide the reference for the understanding of the development mechanism of spikelet and molecular marker for the improvement of ideal spike type in wheat.

Key words: wheat, spike type, auxin, TaARF23-A, spikelet, molecular marker

Table 1

Primers related TaARF23"

引物名称
Primer name		 正向引物
Forward sequence (5′-3′)		 反向引物
Reverse sequence (5′-3′)		 退火温度
Tm (℃)		 扩增长度
Size (bp)
A1-q CGAAGCTTGGAGGTATGTATC GTGCTAATGCACATGGCTTG 58 177
A2-q GCGAAGCTTGGAGGTCGTT GTGCTAATGCACATGGCTTG 58 169
P1 GCCAATCAAGCAAGGATGTC CTGGTGGACAGCAGTGATC 58 951
P2 CGAGGAAGCTTCAGTTACAC TTCTCTGGACAGGTGATACC 58 927
InDel GCAGGAAGAAATCAATGAAGCAG GTAGTAGGTCACTTGGAATTGC 58 82/70

Fig. 1

Spike morphology of wheat lines SY95-71 and CH7034"

Fig. 2

Comparison of the content of five compounds in the auxin synthesis pathway between young spikes of SY95-71 and CH7034 TRP: Tryptophan; TRA: Tryptamine; IAM: Indole-3-acetamide; IAN: Indole-3-acetonitrile; IAA: Indole-3-acetic acid; **: P < 0.01."

Fig. 3

GO enrichment related to auxin pathway in young spike of SY95-71 and CH7034 BP: biological process; MF: molecular function. The unique item numbers are represented in bold. *: P < 0.05; **: P < 0.01."

Fig. 4

DEGs related to auxin pathway in young spike of SY95-71 DEGs with extremely significant differences (| log2(FPKMSY/ FPKMCH) | > 4) are marked with triangles."

Fig. 5

Analysis of TaARF23-A a: sequence analysis and primer positions of TaARF23-A1 and TaARF23-A2. CS: Chinese Spring. b-c: the relative expression level of TaARF23-A1 and TaARF23-A2 in young spikes of SY95-71 and CH7034; ***: P < 0.001, ****: P < 0.0001. d: sequencing results of PCR products amplified by primers P1 and P2 in CH7034 (CH) and SY95-71 (SY). e: the InDel marker of TaARF23-A; M: DNA ladder marker; arrows indicate polymorphic bands."

Fig. 6

Correlation analysis between genotypes of InDel marker and phenotypes of spike in RILs population under six environments S: SY-type band; C: CH-type band; 14C: Chengdu in 2014; 15C: Chengdu in 2015; 16Y1: plot 1 in Yuncheng in 2016; 16Y2: plot 2 in Yuncheng in 2016; 15L: Linfen in 2015; 16L: Linfen in 2016; BLUP: average data for six environments; *: P < 0.05; **: P < 0.01; ****: P < 0.0001."

Fig. 7

Predictive target genes for TaARF23-A a: TaARF23-A regulates TaIAA positively; b: TaARF23-A nega-tively regulates TaSAUR. Transcriptic data of TaSAUR was screened by | log2 (FPKMSY/FPKMCH) | ≤ 1. The vertical bar in the pro-moter region represents the binding element AuxRE of the ARF protein."

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